Setup

Data Description

*GC content of each library showing uneven and 'spikey' patterns. Peaks on the RHS indicate potential incomplete rRNA removal, whilst the other indicate possible excessive PCR cycles and high levels of duplicated sequences.*

GC content of each library showing uneven and ‘spikey’ patterns. Peaks on the RHS indicate potential incomplete rRNA removal, whilst the other indicate possible excessive PCR cycles and high levels of duplicated sequences.

*STAR Alignment summary showing very low levels of unique alignments, which is again suggestive of incomplete rRNA removal. Uniquely mapping reads are now within the range usually seen after summarising to genes*

STAR Alignment summary showing very low levels of unique alignments, which is again suggestive of incomplete rRNA removal. Uniquely mapping reads are now within the range usually seen after summarising to genes

After summarisation the library sizes ranged between 6,954,273 and 14,565,667

Analysis

## Importance of components:
##                            PC1     PC2     PC3      PC4      PC5       PC6
## Standard deviation     69.5070 45.8828 28.5379 19.34833 15.64034 9.792e-14
## Proportion of Variance  0.5772  0.2515  0.0973  0.04473  0.02923 0.000e+00
## Cumulative Proportion   0.5772  0.8287  0.9261  0.97077  1.00000 1.000e+00
Top ranked genes
ID Name logFC AveExpr t P.Value FDR Location
ENSRNOG00000047551 Pnpla2 -7.193 0.1297 -13.55 3.224e-06 0.02734 1:213997709-214002815:(+)
ENSRNOG00000050004 LOC100909761 6.555 -1.417 13.04 4.155e-06 0.02734 9:37727942-37747514:(+)
ENSRNOG00000032832 Mmp10 3.502 2.164 9.505 3.31e-05 0.1411 8:5734348-5742243:(+)
ENSRNOG00000032626 Mmp3 3.614 4.589 8.851 5.236e-05 0.1411 8:5676665-5698579:(+)
ENSRNOG00000002802 Cxcl1 4.896 1.902 8.303 7.86e-05 0.1411 14:18743685-18745457:(-)
ENSRNOG00000010278 Il6 4.791 0.1518 8.274 8.035e-05 0.1411 4:3043231-3047807:(+)
ENSRNOG00000007545 Angptl4 1.852 3.859 8.232 8.3e-05 0.1411 7:18627808-18634079:(-)
ENSRNOG00000060849 Rcor2 -5.115 -1.303 -8.129 8.987e-05 0.1411 1:222519615-222524779:(+)
ENSRNOG00000000239 Ccl7 2.753 2.899 8.037 9.652e-05 0.1411 10:69423086-69424979:(+)
ENSRNOG00000024705 Rarres2 2.478 4.591 7.585 0.0001388 0.1548 4:78205812-78208767:(-)

Genes to an FDR of 15.0%

Genes to an FDR of 15.0%

Genes up to an FDR of 20\%

Genes up to an FDR of 20%

Session Info

R version 3.5.2 (2018-12-20)

**Platform:** x86_64-pc-linux-gnu (64-bit)

locale: LC_CTYPE=en_AU.UTF-8, LC_NUMERIC=C, LC_TIME=en_AU.UTF-8, LC_COLLATE=en_AU.UTF-8, LC_MONETARY=en_AU.UTF-8, LC_MESSAGES=en_AU.UTF-8, LC_PAPER=en_AU.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_AU.UTF-8 and LC_IDENTIFICATION=C

attached base packages: stats4, parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: ggrepel(v.0.8.0), plyranges(v.1.2.0), rtracklayer(v.1.42.2), GenomicRanges(v.1.34.0), GenomeInfoDb(v.1.18.2), IRanges(v.2.16.0), S4Vectors(v.0.20.1), scales(v.1.0.0), ngsReports(v.0.99.7), BiocGenerics(v.0.28.0), pander(v.0.6.3), magrittr(v.1.5), forcats(v.0.4.0), stringr(v.1.4.0), dplyr(v.0.8.0.1), purrr(v.0.3.2), readr(v.1.3.1), tidyr(v.0.8.3), tibble(v.2.1.1), ggplot2(v.3.1.0), tidyverse(v.1.2.1), edgeR(v.3.24.3) and limma(v.3.38.3)

loaded via a namespace (and not attached): nlme(v.3.1-137), bitops(v.1.0-6), matrixStats(v.0.54.0), lubridate(v.1.7.4), RColorBrewer(v.1.1-2), httr(v.1.4.0), tools(v.3.5.2), backports(v.1.1.3), R6(v.2.4.0), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.1.2), tidyselect(v.0.2.5), compiler(v.3.5.2), cli(v.1.1.0), rvest(v.0.3.2), Biobase(v.2.42.0), Cairo(v.1.5-9), xml2(v.1.2.0), DelayedArray(v.0.8.0), plotly(v.4.8.0), ggdendro(v.0.1-20), labeling(v.0.3), digest(v.0.6.18), Rsamtools(v.1.34.1), rmarkdown(v.1.12), XVector(v.0.22.0), pkgconfig(v.2.0.2), htmltools(v.0.3.6), highr(v.0.8), htmlwidgets(v.1.3), rlang(v.0.3.2), readxl(v.1.3.1), rstudioapi(v.0.10), shiny(v.1.2.0), generics(v.0.0.2), zoo(v.1.8-5), hwriter(v.1.3.2), jsonlite(v.1.6), crosstalk(v.1.0.0), BiocParallel(v.1.16.6), RCurl(v.1.95-4.12), GenomeInfoDbData(v.1.2.0), Matrix(v.1.2-17), Rhdf5lib(v.1.4.3), Rcpp(v.1.0.1), munsell(v.0.5.0), stringi(v.1.4.3), yaml(v.2.2.0), MASS(v.7.3-51.1), SummarizedExperiment(v.1.12.0), zlibbioc(v.1.28.0), rhdf5(v.2.26.2), plyr(v.1.8.4), grid(v.3.5.2), promises(v.1.0.1), crayon(v.1.3.4), lattice(v.0.20-38), Biostrings(v.2.50.2), haven(v.2.1.0), hms(v.0.4.2), locfit(v.1.5-9.1), knitr(v.1.22), pillar(v.1.3.1), XML(v.3.98-1.19), glue(v.1.3.1), evaluate(v.0.13), ShortRead(v.1.40.0), latticeExtra(v.0.6-28), data.table(v.1.12.0), modelr(v.0.1.4), httpuv(v.1.5.0), cellranger(v.1.1.0), gtable(v.0.3.0), assertthat(v.0.2.1), xfun(v.0.5), mime(v.0.6), xtable(v.1.8-3), broom(v.0.5.1), later(v.0.8.0), viridisLite(v.0.3.0), truncnorm(v.1.0-8) and GenomicAlignments(v.1.18.1)